Lee Cattermole's first Premiership goal was enough to give Middlesbrough victory in a dismal match at Eastlands.
Lee Cattermole celebrates his winning strike at Eastlands
The midfielder's neat header from Stewart Downing's cross was the only chance of note in a dire first half.
The tempo increased in the second period as Yakubu, Cattermole and James Morrison all went close, with Boro firmly in control.
Manchester City keeper David James made four fine saves but one goal was enough for Boro to clinch a win.
Middlesbrough gained their morale-boosting win on the back of the disappointing defeat in Basle on Thursday, while Manchester City again failed to record their first victory over Boro in the Premiership.
The slippery conditions at Eastlands made for a scrappy opening, with both sides cancelling out each other in a tepid first period.
Boro's already depleted side was given further problems when Franck Queudrue limped off after only nine minutes after the defender challenged for the ball with City striker Darius Vassell.
The home fans were given little to get excited about until Albert Riera's trickery down the left produced a near-post cross that Trevor Sinclair just failed to direct on target.
And, with chances at a premium, Vassell would have been disappointed not to have put his shot away after being put clean through by Stephen Ireland, while Riera's low, left-foot drive just fizzed past the post soon afterwards.
But it was the visiting side that took the lead three minutes before the break - in the only moment of quality during the first half.
Downing's pinpoint cross found the head of the onrushing Cattermole, who headed in his landmark goal.
Much to the frustration of the home faithful, the second half started with the same apathy as the first 45 minutes.
But Cattermole could have scored his and Boro's second goal 10 minutes after the break - only for James to twice repel the midfielder's efforts after being put clean through by Yakubu.
Yakubu himself had two chances to put the game beyond City as Steve McClaren's side took full control of proceedings.
With Middlesbrough in charge, the chances began to flow and Morrison should have punished the City defence on two occasions but a combination of a James save and a wayward swipe kept the deficit to one.
Every Boro attack threatened the City goal and, with the home side in disarray, Stuart Parnaby and Fabio Rochemback should have increased the lead but Boro cantered home.
Man City: James, Danny Mills, Dunne, Richards, Thatcher, Sinclair (Croft 66), Sibierski (Flood 72), Ireland (Musampa 60), Riera, Vassell, Samaras.
Subs Not Used: Sommeil, Wright-Phillips.
Middlesbrough: Jones, Parnaby, Ehiogu, Riggott, Queudrue (Taylor 9), Morrison (Davies 89), Cattermole, Boateng, Rochemback, Downing, Yakubu.
Subs Not Used: Knight, Mendieta, Viduka.
Goals: Cattermole 42.
Ref: M Riley (W Yorkshire).